[2024-01-25 18:39:35,673] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:35,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:35,675] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc3ba7af-4ded-4fa8-911e-87bdfa2b05c5/dqc_reference
[2024-01-25 18:39:36,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:36,789] [INFO] Task started: Prodigal
[2024-01-25 18:39:36,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f68afa7-d368-43b3-a772-41992004ff90/GCF_002263515.1_ASM226351v1_genomic.fna.gz | prodigal -d GCF_002263515.1_ASM226351v1_genomic.fna/cds.fna -a GCF_002263515.1_ASM226351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:54,877] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:54,877] [INFO] Task started: HMMsearch
[2024-01-25 18:39:54,877] [INFO] Running command: hmmsearch --tblout GCF_002263515.1_ASM226351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc3ba7af-4ded-4fa8-911e-87bdfa2b05c5/dqc_reference/reference_markers.hmm GCF_002263515.1_ASM226351v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:55,130] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:55,131] [INFO] Found 6/6 markers.
[2024-01-25 18:39:55,173] [INFO] Query marker FASTA was written to GCF_002263515.1_ASM226351v1_genomic.fna/markers.fasta
[2024-01-25 18:39:55,173] [INFO] Task started: Blastn
[2024-01-25 18:39:55,173] [INFO] Running command: blastn -query GCF_002263515.1_ASM226351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc3ba7af-4ded-4fa8-911e-87bdfa2b05c5/dqc_reference/reference_markers.fasta -out GCF_002263515.1_ASM226351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:56,349] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:56,352] [INFO] Selected 12 target genomes.
[2024-01-25 18:39:56,353] [INFO] Target genome list was writen to GCF_002263515.1_ASM226351v1_genomic.fna/target_genomes.txt
[2024-01-25 18:39:56,361] [INFO] Task started: fastANI
[2024-01-25 18:39:56,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f68afa7-d368-43b3-a772-41992004ff90/GCF_002263515.1_ASM226351v1_genomic.fna.gz --refList GCF_002263515.1_ASM226351v1_genomic.fna/target_genomes.txt --output GCF_002263515.1_ASM226351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:11,712] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:11,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc3ba7af-4ded-4fa8-911e-87bdfa2b05c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:11,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc3ba7af-4ded-4fa8-911e-87bdfa2b05c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:11,722] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:40:11,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:11,722] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Actinopolyspora erythraea	strain=YIM 90600	GCA_002263515.1	414996	414996	type	True	100.0	1745	1747	95	conclusive
Actinopolyspora erythraea	strain=YIM 90600	GCA_000763095.1	414996	414996	type	True	99.9715	1732	1747	95	conclusive
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	94.4673	1467	1747	95	below_threshold
Actinopolyspora righensis	strain=DSM 45501	GCA_900116555.1	995060	995060	type	True	87.0048	1383	1747	95	below_threshold
Actinopolyspora alba	strain=DSM 45004	GCA_900112765.1	673379	673379	type	True	86.8302	1406	1747	95	below_threshold
Actinopolyspora biskrensis	strain=CECT 8576	GCA_013408175.1	1470178	1470178	type	True	81.968	1067	1747	95	below_threshold
Actinopolyspora halophila	strain=DSM 43834	GCA_000371785.1	1850	1850	type	True	81.9374	1040	1747	95	below_threshold
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	79.5447	745	1747	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	79.5009	739	1747	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000171635.1	1836	1836	type	True	79.4513	726	1747	95	below_threshold
Saccharopolyspora rectivirgula	strain=DSM 43747	GCA_000497205.1	28042	28042	type	True	78.7709	510	1747	95	below_threshold
Amycolatopsis panacis	strain=YIM PH21725	GCA_003600245.1	2340917	2340917	type	True	77.2659	333	1747	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:11,724] [INFO] DFAST Taxonomy check result was written to GCF_002263515.1_ASM226351v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:11,724] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:11,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:11,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc3ba7af-4ded-4fa8-911e-87bdfa2b05c5/dqc_reference/checkm_data
[2024-01-25 18:40:11,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:11,778] [INFO] Task started: CheckM
[2024-01-25 18:40:11,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002263515.1_ASM226351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002263515.1_ASM226351v1_genomic.fna/checkm_input GCF_002263515.1_ASM226351v1_genomic.fna/checkm_result
[2024-01-25 18:41:20,606] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:20,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:20,642] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:20,643] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:20,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002263515.1_ASM226351v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:20,644] [INFO] Task started: Blastn
[2024-01-25 18:41:20,644] [INFO] Running command: blastn -query GCF_002263515.1_ASM226351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc3ba7af-4ded-4fa8-911e-87bdfa2b05c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002263515.1_ASM226351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:22,505] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:22,508] [INFO] Selected 8 target genomes.
[2024-01-25 18:41:22,509] [INFO] Target genome list was writen to GCF_002263515.1_ASM226351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:22,514] [INFO] Task started: fastANI
[2024-01-25 18:41:22,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f68afa7-d368-43b3-a772-41992004ff90/GCF_002263515.1_ASM226351v1_genomic.fna.gz --refList GCF_002263515.1_ASM226351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002263515.1_ASM226351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:33,439] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:33,445] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:33,446] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002263515.1	s__Actinopolyspora erythraea	100.0	1745	1747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_900104475.1	s__Actinopolyspora xinjiangensis	94.4536	1468	1747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116555.1	s__Actinopolyspora righensis	87.0079	1383	1747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	98.44	98.44	0.91	0.91	2	-
GCF_900112765.1	s__Actinopolyspora alba	86.8351	1405	1747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	N/A	N/A	N/A	N/A	1	-
GCF_900101095.1	s__Actinopolyspora mzabensis	86.4625	1322	1747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100925.1	s__Actinopolyspora saharensis	82.2676	1047	1747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	98.98	98.97	0.92	0.92	3	-
GCF_006716775.1	s__Actinopolyspora sp006716775	82.1013	1023	1747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408175.1	s__Actinopolyspora biskrensis	81.9449	1070	1747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:33,447] [INFO] GTDB search result was written to GCF_002263515.1_ASM226351v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:33,448] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:33,450] [INFO] DFAST_QC result json was written to GCF_002263515.1_ASM226351v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:33,451] [INFO] DFAST_QC completed!
[2024-01-25 18:41:33,451] [INFO] Total running time: 0h1m58s